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Download BioPharmics Surflex Platform 2025 Build 5.197
BioPharmics Surflex Platform software full crack download, The Surflex Platform consists of the five modules described below for Computational Tools for Drug Discovery. The Surflex Manual contains details of all computational procedures and options within each command-line module. All of the modules are multi-core capable, and very substantial speed-ups are observed with modern multi-core laptops, workstations, and HPC clusters.
leading solutions in the areas of 2D to 3D ligand conversion and conformer generation (FGen3D and ForceGen), molecular docking (Surflex-Dock), molecular similarity (eSim), binding affinity prediction (QuanSA), and real-space modeling of ligand ensembles in X-ray density maps. All methods within the Surflex platform couple physical realism in modeling protein-ligand interactions with algorithms for rapid optimization of conformation and alignment of small molecules.
Tools Module
The Tools module is focused on preparing and processing small molecules. It offers a suite of features that ensures fast and accurate handling of molecular data.
Features and Benefits:
- 2D to 3D Conversion: Transforms SMILES or SDF input into 3D structures.
- Chirality Detection: Identifies and enumerates chiral centers.
- Protonation: Adjusts protonation states of molecules.
- Conformer Generation: Produces diverse conformations of molecules.
This module uses the MMFF94sf forcefield for structure derivation, ensuring high accuracy. It’s especially adept at processing macrocyclic ligands and can incorporate NMR restraints, which is crucial for large peptidic macrocycles.
Similarity Module
The Similarity module excels in performing 3D molecular similarity operations using the eSim method, making it an invaluable tool for virtual screening and pose prediction.
Features and Benefits:
- Virtual Screening: Efficiently screens large molecular databases, with speeds exceeding 20 million compounds per day on a single core.
- Pose Prediction: Provides highly accurate pose predictions.
- Multiple Ligand Alignment: Aligns multiple ligands for comparative analysis.
The module’s virtual screening capabilities are practically and statistically superior, making it a powerful tool for high-throughput screening.
Docking and xGen Modules
These modules provide a comprehensive solution for virtual screening, pose prediction, and X-ray density modeling of ligands.
Docking Module Features:
- PDB Retrieval: Automates large-scale retrieval and processing of PDB structures.
- Binding Site Alignment: Uses PSIM for surface-based alignment.
- Pocket Variant Selection: Automatically selects relevant protein conformations for virtual screening.
- Large-scale PDB retrieval and processing
- Surface-based binding site alignment using the PSIM method
Fully automatic pocket variant selection to cover the relevant protein conformational variation - Virtual screening
- Pose prediction
XGen Module Features:
- Ligand Density Modeling: Uses conformational ensembles for real-space refinement.
- X-ray Density Fitting: Produces chemically sensible conformers with low strain energy, improving fit to X-ray density.
These modules are highly validated and can handle both non-macrocyclic and macrocyclic ligands with high accuracy.
Affinity Module
The Affinity module uses the QuanSA method for predicting binding affinity and ligand pose, integrating machine learning to enhance predictive accuracy.
Features and Benefits:
- Binding Affinity Prediction: Quantitatively predicts binding affinity using physical models.
- Pose Prediction: Accurately predicts ligand binding modes.
- Model Refinement: Iteratively refines models with new data, improving accuracy over time.
This module builds comprehensive models that approximate the causal basis of protein-ligand interactions, making it a unique and powerful tool for drug discovery.
BioPharmics Surflex Platform software details:
- Operating system: Windows x64, Linux and macOS
- File Size: 2.78 GB
- Crack: Full Crack (unlimited PC)
